Foreword ..................................................... xiii
Preface ........................................................ xv
Contributors ................................................. xvii
PART I COORDINATION CHEMISTRY IN NATIVE PROTEIN CAGES
1 The Chemistry of Nature's Iron Biominerals in Ferritin
Protein Nanocages ............................................ 3
Elizabeth C. Theil and Rabindra K. Behera
1.1 Introduction ............................................ 3
1.2 Ferritin Ion Channels and Ion Entry ..................... 6
1.2.1 Maxi-and Mini-Ferritin ........................... 6
1.2.2 Iron Entry ....................................... 7
1.3 Ferritin Catalysis ...................................... 8
1.3.1 Spectroscopic Characterization of μ-1,2
Peroxodiferric Intermediate (DFP) ................ 8
1.3.2 Kinetics of DFP Formation and Decay ............. 12
1.4 Protein-Based Ferritin Mineral Nucleation and Mineral
Growth ................................................. 13
1.5 Iron Exit .............................................. 16
1.6 Synthetic Uses of Ferritin Protein Nanocages ........... 17
1.6.1 Nanomaterials Synthesized in Ferritins .......... 18
1.6.2 Ferritin Protein Cages in Metalloorganic
Catalysis and Nanoelectronics ................... 19
1.6.3 Imaging and Drug Delivery Agents Produced in
Ferritins ....................................... 19
1.7 Summary and Perspectives .............................. 20
Acknowledgments ............................................. 20
References .................................................. 21
2 Molecular Metal Oxides in Protein Cages/Cavities ............ 25
Achim Müler and Dieter Rehder
2.1 Introduction ........................................... 25
2.2 Vanadium: Functional Oligovanadates and Storage of
VO2+ in Vanabins ....................................... 26
2.3 Molybdenum and Tungsten: Nucleation Process in
a Protein Cavity ....................................... 28
2.4 Manganese in Photosystem II ............................ 33
2.5 Iron: Ferritins, DPS Proteins, Frataxins, and
Magnetite .............................................. 35
2.6 Some General Remarks: Oxides and Sulfides .............. 38
References .................................................. 38
PART II DESIGN OF METALLOPROTEIN CAGES
3 De Novo Design of Protein Cages to Accommodate
Metal Cofactors ............................................. 45
Flavia Nastri, Rosa Bruni, Omella Maglio, and Angela Lombardi
3.1 Introduction ........................................... 45
3.2 De Novo-Designed Protein Cages Housing Mononuclear
Metal Cofactors ........................................ 47
3.3 De Novo-Designed Protein Cages Housing Dinuclear
Metal Cofactors ........................................ 59
3.4 De Novo-Designed Protein Cages Housing Heme Cofactor ... 66
3.5 Summary and Perspectives ............................... 79
Acknowledgments ............................................. 79
References .................................................. 80
4 Generation of Functionalized Biomolecules Using
Hemoprotein Matrices with Small Protein Cavities for
Incorporation of Cofactors .................................. 87
Takashi Hayashi
4.1 Introduction ........................................... 87
4.2 Hemoprotein Reconstitution with an Artificial Metal
Complex ................................................ 89
4.3 Modulation of the O2 Affinity of Myoglobin ............. 90
4.4 Conversion of Myoglobin into Peroxidase ................ 95
4.4.1 Construction of a Substrate-Binding Site Near
the Heme Pocket ................................. 95
4.4.2 Replacement of Native Heme with Iron
Porphyrinoid in Myoglobin ....................... 99
4.4.3 Other Systems Used in Enhancement of
Peroxidase Activity of Myoglobin ............... 100
4.5 Modulation of Peroxidase Activity of HRP .............. 102
4.6 Myoglobin Reconstituted with a Schiff Base Metal
Complex ............................................... 103
4.7 A Reductase Model Using Reconstituted Myoglobin ....... 106
4.7.1 Hydrogenation Catalyzed by Cobalt Myoglobin .... 106
4.7.2 A Model of Hydrogenase Using the Heme Pocket
of Cytochrome с ................................ 107
4.8 Summary and Perspectives .............................. 108
Acknowledgments ............................................ 108
References ................................................. 108
5 Rational Design of Protein Cages for Alternative Enzymatic
Functions .................................................. 111
Nicholas M. Marshall, Kyle D. Miner, Tiffany D. Wilson,
and Yi Lu
5.1 Introduction .......................................... 111
5.2 Mononuclear Electron Transfer Cupredoxin Proteins ..... 112
5.3 Cua Proteins .......................................... 116
5.4 Catalytic Copper Proteins ............................. 118
5.4.1 Type 2 Red Copper Sites ........................ 118
5.4.2 Other T2 Copper Sites .......................... 120
5.4.3 Cu, Zn Superoxide Dismutase .................... 121
5.4.4 Multicopper Oxygenases and Oxidases ............ 122
5.5 Heme-Based Enzymes .................................... 124
5.5.1 Mb-Based Peroxidase and P450 Mimics ............ 124
5.5.2 Mimicking Oxidases in Mb ....................... 125
5.5.3 Mimicking NOR Enzymes in Mb .................... 127
5.5.4 Engineering Peroxidase Proteins ................ 128
5.5.5 Engineering Cytochrome P450s ................... 129
5.6 Non-Heme ET Proteins .................................. 131
5.7 Fe And Mn Superoxide Dismutase ........................ 132
5.8 Non-Heme Fe Catalysts ................................. 133
5.9 Zinc Proteins ......................................... 134
5.10 Other Metalloproteins ................................. 135
5.10.1 Cobalt Proteins ................................ 135
5.10.2 Manganese Proteins ............................. 136
5.10.3 Molybdenum Proteins ............................ 137
5.10.4 Nickel Proteins ................................ 137
5.10.5 Uranyl Proteins ................................ 138
5.10.6 Vanadium Proteins .............................. 138
5.11 Summary and Perspectives .............................. 139
Rreferences ................................................... 142
PART III COORDINATION CHEMISTRY OF PROTEIN ASSEMBLY CAGES
6 Metal-Directed and Templated Assembly of Protein
Superstructures and Cages .................................. 151
F. Akif Tezcan
6.1 Introduction .......................................... 151
6.2 Metal-Directed Protein Self-Assembly .................. 152
6.2.1 Background ..................................... 152
6.2.2 Design Considerations for Metal-Directed
Protein Self-Assembly .......................... 153
6.2.3 Interfacing Non-Natural Chelates with MDPSA .... 155
6.2.4 Crystallographic Applications of Metal-
Directed Protein Self-Assembly ................. 159
6.3 Metal-Templated Interface Redesign ....................... 162
6.3.1 Background ..................................... 162
6.3.2 Construction of a Zn-Selective Tetrameric
Protein Complex Through MeTIR .................. 163
6.3.3 Construction of a Zn-Selective Protein
Dimerization Motif Through MeTIR ............... 166
6.4 Summary and Perspectives .............................. 170
Acknowledgments ............................................... 171
References .................................................... 171
7 Catalytic Reactions Promoted in Protein Assembly Cages ..... 175
Takafumi Ueno and Satoshi Abe
7.1 Introduction .......................................... 175
7.1.1 Incorporation of Metal Compounds ............... 176
7.1.2 Insight into Accumulation Process of Metal
Compounds ...................................... 177
7.2 Ferritin as a Platform for Coordination Chemistry ........ 177
7.3 Catalytic Reactions in Ferritin .......................... 179
7.3.1 Olefin Hydrogenation ........................... 179
7.3.2 Suzuki-Miyaura Coupling Reaction in Protein
Cages .......................................... 182
7.3.3 Polymer Synthesis in Protein Cages ............. 185
7.4 Coordination Processes in Ferritin ....................... 188
7.4.1 Accumulation of Metal Ions ..................... 188
7.4.2 Accumulation of Metal Complexes ................ 192
7.5 Coordination Arrangements in Designed Ferritin Cages .. 194
7.6 Summary and Perspectives .............................. 197
Acknowledgments ............................................ 198
References ................................................. 198
8 Metal-Catalyzed Organic Transformations Inside a Protein
Scaffold Using Artificial Metalloenzymes ................... 203
V.K.K. Praneeth and Thomas R. Ward
8.1 Introduction .......................................... 203
8.2 Enantioselective Reduction Reactions Catalyzed by
Artificial Metalloenzymes ............................. 204
8.2.1 Asymmetric Hydrogenation ....................... 204
8.2.2 Asymmetric Transfer Hydrogenation of Ketones ... 206
8.2.3 Artificial Transfer Hydrogenation of Cyclic
Imines ......................................... 208
8.3 Palladium-Catalyzed Allylic Alkylation ................ 211
8.4 Oxidation Reaction Catalyzed by Artificial
Metalloenzymes ........................................ 212
8.4.1 Artificial Sulfoxidase ......................... 212
8.4.2 Asymmetric ds-Dihydroxylation .................. 215
8.5 Summary and Perspectives .............................. 216
References ................................................. 218
PART IV APPLICATIONS IN BIOLOGY
9 Selective Labeling and Imaging of Protein Using Metal
Complex .................................................... 223
Yasutaka Kurishita and Itaru Hamachi
9.1 Introduction .......................................... 223
9.2 Tag-Probe Pair Method Using Metal-Chelation System .... 225
9.2.1 Tetracysteine Motif/Arsenical Compounds Pair ... 225
9.2.2 Oligo-Histidine Tag/Ni(II)-NTA Pair ............ 227
9.2.3 Oligo-Aspartate Tag/Zn(II)-DpaTyr Pair ......... 230
9.2.4 Lanthanide-binding Tag ......................... 235
9.3 Summary and Perspectives .............................. 237
References ................................................. 237
10 Molecular Bioengineering of Magnetosomes for
Biotechnological Applications .............................. 241
Atsushi Arakaki, Michiko Nemoto, and Tadashi Malsunaga
10.1 Introduction .......................................... 241
10.2 Magnetite Biomineralization Mechanism in Magnetosome .. 242
10.2.1 Diversity of Magnetotactic Bacteria ........... 242
10.2.2 Genome and Proteome Analyses of Magnetotactic
Bacteria ...................................... 244
10.2.3 Magnetosome Formation Mechanism ................ 246
10.2.4 Moфhological Control of Magnetite Crystal in
Magnetosomes ................................... 250
10.3 Functional Design of Magnetosomes ..................... 251
10.3.1 Protein Display on Magnetosome by Gene Fusion
Technique ...................................... 252
10.3.2 Magnetosome Surface Modification by In Vitro
System ......................................... 255
10.3.3 Protein-mediated Morphological Control of
Magnetite Particles ............................ 257
10.4 Application ........................................... 258
10.4.1 Enzymatic Вioassays ............................ 259
10.4.2 Cell Separation ................................ 260
10.4.3 DNA Extraction ................................. 262
10.4.4 Bioremediation ................................. 264
10.5 Summary and Perspectives .............................. 266
Acknowledgments ............................................ 266
References ................................................. 266
PART V APPLICATIONS IN NANOTECHNOLOGY
11 Protein Cage Nanoparticles for Hybrid Inorganic-Organic
Materials .................................................. 275
Shefah Qazi, Janice Lucon, Masaki Uchida, and Trevor Douglas
11.1 Introduction .......................................... 275
11.2 Biomineral Formation in Protein Cage Architectures .... 277
11.2.1 Introduction ................................... 277
11.2.2 Mineralization ................................. 278
11.2.3 Model for Synthetic Nucleation-Driven
Mineralization ................................. 279
11.2.4 Mineralization in Dps: A 12-Subunit Protein
Cage ........................................... 279
11.2.5 Icosahedral Protein Cages: Viruses ............. 282
11.2.6 Nucleation of Inorganic Nanoparticles
Within Icosahedral Viruses ..................... 282
11.3 Polymer Formation Inside Protein Cage
Nanoparticles ......................................... 283
11.3.1 Introduction ................................... 283
11.3.2 Azide-Alkyne Click Chemistry in sHsp and
P22 ............................................ 285
11.3.3 Atom Transfer Radical Polymerization in P22 .... 287
11.3.4 Application as Magnetic Resonance Imaging
Contrast Agents ................................ 290
11.4 Coordination Polymers in Protein Cages ................ 292
11.4.1 Introduction ................................... 292
11.4.2 Metal-Organic Branched Polymer Synthesis
by Preforming Complexes ........................ 292
11.4.3 Coordination Polymer Formation from Ditopic
Ligands and Metal Ions ......................... 295
11.4.4 Altering Protein Dynamics by Coordination:
Hsp-Phen-Fe .................................... 296
11.5 Summary and Perspectives .............................. 298
Acknowledgments ............................................ 298
References ................................................. 298
12 Nanoparticles Synthesized and Delivered by Protein in
the Field of Nanotechnology Applications ................... 305
Ichiro Yamashita, Kenji Iwahori, Bin Zheng, and Shinya
Kumagai
12.1 Nanoparticle Synthesis in a Bio-Template .............. 305
12.1.1 NP Synthesis by Cage-Shaped Proteins for
Nanoelectronic Devices and Other
Applications ................................... 305
12.1.2 Metal Oxide or Hydro-Oxide NP Synthesis in the
Apoferritin Cavity ............................. 307
12.1.3 Compound Semiconductor NP Synthesis in the
Apoferritin Cavity ............................. 308
12.1.4 NP Synthesis in the Apoferritin with the
Metal-Binding Peptides ......................... 311
12.2 Site-Directed Placement of NPs ........................ 312
12.2.1 Nanopositioning of Cage-Shaped Proteins ........ 312
12.2.2 Nanopositioning of Au NPs by Porter Proteins ... 313
12.3 Fabrication of Nanodevices by the NP and Protein
Conjugates ............................................ 317
12.3.1 Fabrication of Floating Nanodot Gate Memory .... 318
12.3.2 Fabrication of Single-Electron Transistor
Using Ferritin ................................. 321
References ................................................. 326
13 Engineered "Cages" for Design of Nanostructured
Inorganic Materials ........................................ 329
Patrick B. Dennis, Joseph M. Slocik, and Rajesh R. Naik
13.1 Introduction .......................................... 329
13.2 Metal-Binding Peptides ................................ 331
13.3 Discrete Protein Cages ................................ 332
13.4 Heat-Shock Proteins ................................... 334
13.5 Polymeric Protein and Carbohydrate Quasi-Cages ........ 340
13.6 Summary and Perspectives .............................. 346
References ................................................. 347
PART VI COORDINATION CHEMISTRY INSPIRED BY PROTEIN CAGES
14 Metal-Organic Caged Assemblies ............................. 353
Sota Sato and Makoto Fujita
14.1 Introduction .......................................... 353
14.2 Construction of Polyhedral Skeletons by Coordination
Bonds ................................................. 355
14.2.1 Geometrical Effect on Products ................. 356
14.2.2 Structural Extension Based on Rigid,
Designable Framework ........................... 358
14.2.3 Mechanistic Insight into Self-Assembly ......... 366
14.3 Development of Functions via Chemical Modification .... 366
14.3.1 Chemistry in the Hollow of Cages ............... 367
14.3.2 Chemistry on the Periphery of Cages ............ 368
14.4 Metal-Organic Cages for Protein Encapsulation ......... 370
14.5 Summary and Perspectives .............................. 370
References ................................................. 371
Index ......................................................... 375
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